Digital Biology: A survey of topics in bioinformatics and functional genomics
BIOL-L 388 Spring 2018
Course description
BIOL L388 DB
Class times and locations
Tues, Thur 11:15a - 12:30p (Credits: 3.0); Sycamore Hall (SY) 004
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER | Tues | Jan 9 | 0.1 | Orientation What is Digital Biology? MIT video: Introduction to Computational and Systems Biology | Volker Brendel |
| Thur | Jan 11 | 1.1 | Review: Nucleic Acids and Proteins | Volker Brendel |
| Tues | Jan 16 | 1.2 | Bioinformatics Databases and Computing Resources National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics Current Topics in Genome Analysis 2016, a National Human Genome Research Institute lecture series: The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green) Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) | Volker Brendel |
| Thur | Jan 18 | 1.3 | Quiz 1 | Students |
| Tues | Jan 23 | 2.1 | Sequence Alignments 1 How Do We Compare Biological Sequences? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | Jan 25 | 2.2 | Sequence Alignments 2 MIT video: Local Alignment (BLAST) and Statistics | Volker Brendel |
| Tues | Jan 30 | 2.3 | Sequence Alignments 3 MIT video: Global Alignment of Protein Sequences (NW,SW, PAM, BLOSUM) | Volker Brendel |
| Thur | Feb 1 | 2.4 | Quiz 2 | Students |
| Tues | Feb 6 | 3.1 | Evolutionary Processes 1 Introduction to Molecular Evolution The Fastest Outbreak Transforming Distance Matrices into Evolutionary Trees Toward an Algorithm for Distance-Based Phylogeny Construction Additive Phylogeny Using Least-Squares To Construct Distance-Based Phylogenies Ultrametric Trees The Neighbor-Joining Algorithm The powers and pitfalls of parsimony General science/engineering interest: SpaceX Falcon Heavy launch today | Volker Brendel |
| Thur | Feb 8 | 3.2 | Evolutionary Processes 2 Character-based Tree Reconstruction The Small Parsimony Problem The Large Parsimony Problem Evolutionary Tree Reconstruction in the Modern Era | Volker Brendel |
| Tues | Feb 13 | 3.3 | Evolutionary Processes 3 EBI MSA Tools EBI MP Tools | Volker Brendel |
| Thur | Feb 15 | 3.4 | Quiz 3 | Students |
| Tues | Feb 20 | 4.1 | Genome Characteristics 1 (Motivation) The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green) | Volker Brendel |
| Thur | Feb 22 | 4.2 | Genome Characteristics 2 (Assembly) Introduction to genome sequencing How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Tues | Feb 27 | 4.3 | Genome Characteristics 3 (Assembly, continued) | Volker Brendel |
| Thur | March 1 | 4.4 | Quiz 4 | Students |
| Tues | March 6 | 5.1 | Genome Annotation: Introduction NCBI Genome: Deinococcus radiodurans GFF3 standard GeneMark.hmm prokaryotic GeneMark article | Volker Brendel |
| Thur | March 8 | 5.2 | Genome Annotation: Practice GeneMark AUGUSTUS GENSCAN paper wasp genome browser | Volker Brendel |
| Tues | March 13 | Spring Break | ||
| Thur | March 15 | Spring Break | ||
| Tues | March 20 | 5.3 | Hidden Markov Models: Concepts and Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Thur | March 22 | 5.4 | Quiz 5 | Students |
| Tues | March 27 | 6.1 | Protein Structures 1 PDB: What is a protein? PDB: How enzymes work HIV I HIV II Guide to PDB PDB Molecule of the Month NCBI Protein MIT Lecture: Introduction to Protein Structure; Structure Comparison and Classification | Volker Brendel |
| Thur | March 29 | 6.2 | Protein Structures 2: Secondary Structure 2struct server Jpred - secondary structure prediction Stride SPIDER2 | Dr. Thomas McCarthy |
| Tues | April 3 | 6.3 | Protein Structures 3 MIT Lecture: Predicting Protein Structure | Volker Brendel |
| Thur | April 5 | 6.4 | Quiz 6 | Students |
| Tues | April 10 | 6.5 | Protein Structures 4 MIT Lecture: Predicting Protein Interactions | Volker Brendel |
| Thur | April 12 | 6.6 | Protein Structures 5 foldit | Volker Brendel |
| Tues | April 17 | 7.1 | Cells and Organisms 1 MIT Lecture: Gene Regulatory Networks | Volker Brendel |
| Thur | April 19 | 7.2 | Cells and Organisms 2 Course Questionnaire | Volker Brendel |
| Mon | April 23 | 11:59am | Homework Assignment due | Students |
| Tues | April 24 | 8.1 | Review | Volker Brendel |
| Thur | April 26 | 8.2 | Review Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | May 3 | 12:30pm - 2:30pm | Final Examination | Students |